Members of the Flavivirus genus are the most important arthropod-borne viruses causing disease in humans, many of which are characterized as NIH Category A, B, and C organisms. This genus includes viruses [West Nile virus (WNV), Japanese encephalitis virus (JEV) and Dengue virus (DENV)] that are endemic and continue to spread in many areas of the world. Flaviviruses account for -100 millions infections per year, with billions at risk and no specific therapy available. Although much work has focused on understanding the mechanisms of flavivirus replication in cultured cells, and on defining virulence in vivo, less remains known about host responses to strains of different virulence, and the genes and cell types that modulate infection in vivo. Here, we propose to identify and define the mechanism of action of novel host genes that modulate WNV infection. A systems biology approach to studying complex host-pathogen interactions associated with infection by virulent and attenuated WNV strains will provide new insight into host response mechanisms. With the support of several Cores (computational; proteomics, metabolomics, and lipidomics; data management and resources dissemination), we will acquire a global picture of the host response to infection by WNV strains of distinct pathogenic potential. Such an analysis has never been performed for any flavivirus. This approach to studying WNV pathogenesis will interact directly with work in Project 1 on influenza A and Ebola viruses to identify novel common genes, networks, and pathways that restrict infection with the viruses studied here. Target genes identified by systems biology will be validated in cells using ectopic expression and gene silencing, and these phenotypes will help prioritizing the generation of new KO mice for evaluation of the function of target genes in vivo in the context of WNV infection. Overall, our studies will provide new insight into the cellular processes that restrict infection by WNV and likely other viruses, and thus may promote novel strategies for development of therapeutic agents that contain virus spread and disease. Moreover, it may have implications for understanding the genetic variation in humans, which could explain susceptibility to particular viral infections.